Labour claimed the register served as a "damning indictment" of the health reforms which recently passed into law after a bruising parliamentary battle.

The warnings about the threat posed by the bill were issued in a draft version of the risk register, dated 28 September 2010, which was leaked to the health writer Roy Lilley.

The government has been criticised for refusing to comply with a ruling by the information commissioner to publish the Transition Risk Register, drawn up on 10 November 2010, after an FOI request by the former shadow health secretary, John Healey.

The register sets out the risks posed by the health and social care bill which will devolve 60% of the NHS's £100bn budget to new GP-led consortia. The draft version of the register warned of:

• A longer term danger to the NHS's ability to cope with emergencies. It said: "The NHS role in emergency preparedness/responsiveness is more difficult to manage through a more devolved organisation, and so emergencies are less well managed/ mitigated."

• Greater costs if new GP-led consortiums make greater use of the private sector. "One example of area where system could be more costly is if GP Consortia makes use of private sector organisations/staff which adds costs to the overall system."

• A danger that the new system is set up too quickly, threatening the running of the NHS.

• A loss of financial control. "Financial control is lost due to the restructuring of budgets distributed between or allocated to organisations within the system [to be clarified]," it said.

• Unfavourable media coverage. "Public reputation. There is a risk that the transition will be presented in a negative light via the media. Two of the biggest risks which have already surfaced in the media are i) that the reforms will continue to be characterised through the prism of privatisation and ii) financial cuts."

Health secretary Andrew Lansley's reforms were built on demolishing a layer of management – the primary care trusts which currently purchase care on behalf of patients. But the document highlights the risk that the reforms would sow confusion between rival bodies on the ground during the transition to Lansley's new look NHS. Civil servants also rate highly the danger that the £20bn savings may not materialise as managers lose focus and that the quality of patient care suffers.

The Department of Health said that it did not comment on leaks. But it is understood that the leaked document looked familiar to officials. Ministers are likely to argue that the document is an early draft drawn up four months before the publication of the health and social care bill. Since then the bill has undergone two major changes during the government's "listening exercise" last spring and in a series of parliamentary amendments. Ministers will also say that a report to be published on Tuesday shows that the NHS is on course to meet the so called "Nicholson challenge" to save £20bn over the course of this parliament.

But Labour seized on the document. Liz Kendall, the shadow social care minister, said: "This is a damning indictment of the health bill – forced through by the Tories with cover from the Lib Dems. It shows beyond doubt the high risks the bill poses to patients and taxpayers. The government has repeatedly tried to hide these risks, but its own assessment of the bill makes them devastatingly clear. Patients and the public will not forget or forgive David Cameron for his reckless NHS gamble."

Andy Burnham, shadow health secretary, said: "Now we know why David Cameron refused to publish the risk register before the bill was through parliament – it's because civil servants were telling him his reorganisation was likely to cause major damage to the NHS. David Cameron will never be forgiven for knowingly taking these risks with the country's best-loved institution."

Clare Gerada, chair of the Royal College of General Practitioners and a critic of the reforms, tweeted that the risk register was "very scary reading & should have been disclosed long ago".

Healey said: "This is exactly the type of information that the public and parliament lacked while the bill was being debated. This shows how unprepared the NHS and civil service were for this huge NHS reorganisation."

A Department of Health spokesperson said: "We have always been open about risk and have published all relevant information in the impact assessments alongside the bill. As the latest performance figures show we are dealing with those risks, performance is improving – waiting times are down and mixed sex wards are at an all time low - and we are on course to make the efficiency savings that the NHS needs to safeguard it for the future."